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Swiss Roll Reduction with LLE in Scikit-learn

An illustration of Swiss Roll reduction with locally linear embedding

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Version

In [1]:
import sklearn
sklearn.__version__
Out[1]:
'0.18.1'

Imports

In [2]:
import plotly.plotly as py
import plotly.graph_objs as go
from plotly import tools

import numpy as np
import matplotlib.pyplot as plt
from sklearn import manifold, datasets

Calculations

In [3]:
X, color = datasets.samples_generator.make_swiss_roll(n_samples=1500)

print("Computing LLE embedding")
X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12,
                                             n_components=2)
print("Done. Reconstruction error: %g" % err)
Computing LLE embedding
Done. Reconstruction error: 1.3218e-07

Plot Results

In [4]:
def matplotlib_to_plotly(cmap, pl_entries):
    h = 1.0/(pl_entries-1)
    pl_colorscale = []
    
    for k in range(pl_entries):
        C = map(np.uint8, np.array(cmap(k*h)[:3])*255)
        pl_colorscale.append([k*h, 'rgb'+str((C[0], C[1], C[2]))])
        
    return pl_colorscale

cmap = matplotlib_to_plotly(plt.cm.Spectral, 4)

Original Data

In [5]:
try:
    p1 = go.Scatter3d(x=X[:, 0], y=X[:, 1], z=X[:, 2],
                      mode='markers', 
                      marker=dict(color=color, 
                                  colorscale=cmap,
                                  showscale=False,
                                  line=dict(color='black', width=1)))

except:
    p1 = go.Scatter(x=X[:, 0], y=X[:, 2], 
                    mode='markers', 
                    marker=dict(color=color, 
                                colorscale=cmap,
                                showscale=False,
                                line=dict(color='black', width=1)))

layout=dict(title='Original Data',
            margin=dict(l=10, r=10,
                        t=30, b=10)
           )
fig = go.Figure(data=[p1], layout=layout)
In [6]:
py.iplot(fig)
Out[6]:

Projected Data

In [7]:
p2 = go.Scatter(x=X_r[:, 0], y=X_r[:, 1], 
                mode='markers', 
                marker=dict(color=color, 
                            colorscale=cmap,
                            showscale=False,
                            line=dict(color='black', width=1)))
layout=dict(title='Projected Data',
            xaxis=dict(zeroline=False, showgrid=False),
            yaxis=dict(zeroline=False, showgrid=False),
           )
fig = go.Figure(data=[p2], layout=layout)
In [8]:
py.iplot(fig)
Out[8]:

License

Author:

    Fabian Pedregosa -- <fabian.pedregosa@inria.fr>

License:

    BSD 3 clause (C) INRIA 2011
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